The Primordial Inflation Explorer (PIXIE) uses a nulling Fourier Transform Spectrometer to measure the absolute intensity and linear polarization of the cosmic microwave background and diffuse astrophysical foregrounds. PIXIE will search for the signature of primordial inflation and will characterize distortions from a blackbody spectrum, both to precision of a few parts per billion. Rigorous control of potential instrumental effects is required to take advantage of the raw sensitivity. PIXIE employs a highly symmetric design using multiple differential nulling to reduce the instrumental signature to negligible levels. We discuss the systematic error budget and mitigation strategies for the PIXIE mission.